Molecular Dynamics Study of Naturally Occurring Defects in Self-Assembled Monolayer Formation

We address the importance of the dynamic molecular ink concentration at a polymer stamp/substrate interface during microcontact displacement or insertion printing. We demonstrate that by controlling molecular flux, we can influence both the molecular-scale order and the rate of molecular exchange of self-assembled monolayers (SAMs) on gold surfaces. Surface depletion of molecular ink at a polymer stamp/substrate interface is driven predominantly by diffusion into the stamp interior; depletion occurs briefly at the substrate by SAM formation, but diffusion of molecules into the bulk of the stamp dominates over practical experimental time scales. As contact time is increased, the interface concentration varies significantly due to diffusion, affecting the quality and coverage of printed films. Controlling interfacial concentration improves printed film reproducibility and the fractional coverage of multicomponent films can be controlled to within a few percent. We first briefly review the important aspects of molecular ink diffusion at a stamp interface and how it relates to experimental duration. We then describe two examples that illustrate control over ink transfer during experiments: the role of contact time on monolayer reproducibility and molecular order, and the fine control of fractional monolayer coverage for the displacement printing of 1-adamantanethiolate SAMs by 1-dodecanethiol.

The kinetics of the self-assembled monolayer (SAM) formation of 3-mercaptopropionic acid (MPA) on Au surface and of the adsorption of hexadecyltrimethylammonium chloride (C16TAC) on the SAM was investigated by surface-enhanced infrared absorption spectroscopy (SEIRAS) of attenuated total reflection (ATR) mode. The SAM formation of MPA depended on solvents. At the first stage of MPA adsorption in a chloroform-d solution, hydrogen-bonded MPA coexisted with free (non-hydrogen-bonded) MPA which was partly protonated. During the process of the adsorption, the free nonprotonated MPA was protonated or hydrogen-bonded. After the abundant SAM formation, alkyl backbone was rearranged. With adsorption in an ethanol solution, the hydrogen-bonded MPA SAM increased in content without any structural rearrangement. No free species and no protonated species were observed. The molecular orientation was also different between SAMs in chloroform-d and in ethanol. The dependence of the CH2 antisymmetric stretching vibration band intensity on adsorption time was examined on the basis of the adsorption kinetics. It was confirmed that the MPA SAM formation on Au surface proceeds according to the simple Langmuir (monolayer) adsorption theory. On the other hand, the adsorption of C16TAC on the MPA SAM obeyed the kinetics where the fast adsorption at an early stage is followed by the slow adsorption. ATR-SEIRAS indicated that there are the adsorption of C16TAC on the MPA SAM and the transition of carboxylic acid to carboxylate. Finally, ion pairs connected by the electrostatic interaction are formed.

We report the preparation of mixed self-assembled monolayer of 1-octanethiol and 1,10-decanedithiol on Au thin film with preferential Au(111) surface and their characterization using Raman spectroscopy of cysteine adsorbed on mixed self-assembled monolayer mediated isolated Ag nanoparticles. The self-assembled monolayer characterization has been also performed through water contact angle measurement. A significant enhancement in water contact angle from 24° to 103° has been observed on Au surface after self-assembled monolayer formation, primarily due to the hydrophobic nature of the methyl group at the terminal end of the 1-octanethiol, which confirms regular self-assembled monolayer formation. Availability of –SH group from 1,10-decanedithiol on the self-assembled monolayer surface and so, the formation of mixed self-assembled monolayer has been ascertained by immobilization of Ag nanoparticles probed via scanning electron microscopy and Raman spectroscopy of cysteine adsorbed on Ag nanoparticles. Raman spectrum of cysteine on self-assembled monolayer mediated Ag nanoparticles in the fingerprint region of 500–1800 cm−1 shows appreciable increase in the band intensity due to surface enhanced Raman scattering as compared to the band intensity on bare Au surface. These results clearly indicate that the mixed self-assembled monolayer with adequate proportion of component molecules can be utilized as a suitable and inexpensive host for surface enhanced Raman scattering substrates.

Self-assembled monolayer (SAM) formation from decaneselenol on gold substrate surfaces was studied using electrochemical measurements, reflection−absorption Fourier transform infrared spectroscopy (FT-IRRAS), X-ray photoelectron spectroscopy (XPS), and quartz-crystal microbalance (QCM). The Au substrate modified with the SAMs showed clear IR absorption bands corresponding to the CH stretches while distinct photoemission peaks were observed at C 1s, Se 3d, and Se 3p core levels in its XPS spectrum. Using a quartz-crystal microbalance, the surface coverage by the SAM-forming molecule was determined to be 0.88 nmol cm-2. Electrochemical impedance measurements revealed frequency-dependent capacitive behavior of the SAM, and the equivalent parameter was determined to be 6.1 × 10-6 sφ Ω-1 cm-1 (φ = 0.94). It also showed that the surface coverage of 99.8% can be attained, resulting in the suppression of a heterogeneous electron-transfer rate constant for a redox species dissolved in solution phase. The dielectri...

Alkanethiol Self-Assembled Monolayers (SAMs), typically deposited on Au substrates, have been commonly utilized to immobilize receptor biomolecules in the construction of a variety of biosensors, such as the detection of glucose oxidase by the immobilization of calixarenes thiols 1. The appeal of using SAMs derives from their ease of fabrication and component flexibility, allowing for more than one alkanethiol to be deposited in a single monolayer. This results in the formation of SAMs in which each thiol component adds a different property or role, thus introducing versatility to the construction and operation of resulting sensors 2.In our recent work, alkanethiol SAMs, composed of three different thiol molecules, were constructed for use as an electrochemical Toll-Like Receptor 4 (TLR4)-based sensor that can detect Gram-negative bacteria. TLRs are a family of immunoproteins in the innate immune system, which are able to detect a broad category of pathogens, rather than specific targets, as is the case with the adaptive system (e.g., antibodies). In our published work 3, SAMs consisted of a carboxylic acid terminated thiol that allowed for the conversion to a nitrilotriacetic (NTA) group. This moiety could then chelate a Ni2+ cation, followed by attachment of the TLR4 immunoprotein via its His-tag. The second thiol in the SAM contained a terminal ferrocene (Fc) group, where the Fc group was bound to the C11 chain via an amide group. Here, the Fc group serves as a mediator for charge transfer between ferrocyanide in solution and the Au substrate, resulting in relatively high current signals, thus making the sensor potentially field deployable. The third thiol in these SAMs was a hydroxy-terminated thiol, added as a diluent between the immobilized TLR4 receptors. SAMs were prepared by co-deposition on sputter Au on glass.Electrochemical testing involved cyclic voltammetry (CV) studies in pH 7 buffer solution in order to determine the amount of Fc-thiol present, as well as CV and electrochemical impedance spectroscopy (EIS) studies in ferrocyanide solutions to examine its redox-mediation response and to obtain a measure of the charge transfer rate. In the presence of lysed bacteria, the immobilized TLR4 dimerizes, which blocks electrochemical mediation between ferrocyanide and the surface bound Fc. This results in an increase in RCT which is our biosensor signal. However, a key problem with these sensors is that their RCT increased with electrochemical testing in the absence of lysed bacteria, producing signal drift. Thus, in the present work, the reasons for sensor signal drift and methods to overcome it were explored.It was found in recent work that the drift of the full TLR4 sensor was correlated with the loss in the Fc redox signal, although it was not clear if underlying SAM was at the root of the problem. If so, then it was necessary to determine if the loss in the Fc redox activity was caused by the physical loss of the Fc thiol from the Au surface or deactivation of the Fc surface complex and/or its electrochemistry. To determine which of these options was responsible for signal drift, the relative % v/v fraction of the three thiols was varied, and in later work, based on chemical considerations, the Fc molecule containing an amide group was replaced with a C11 chain bonded directly to the Fc. It was found that this latter strategy led to a very stable SAM, showing negligible drift in the Fc CV charges and in the RCT values in ferrocyanide solutions, with or without the TLR4 receptor attached on the outer surface of the SAM.This presentation will focus on presenting the electrochemistry of the various binary and ternary thiol SAMs investigated in this work and examining the Fc CV peak charges, potential, and kinetics, as well as the double layer capacitance, to better understand how and why the Fc redox response was stabilized. This is important because this correlates directly with the stability of the TLR4/Gram-negative bacteria sensor, as will be demonstrated for a TLR2 biosensor tested against Gram-positive bacteria cell wall ligands.

Formation of self-assembled monolayers (SAMs) of three porphyrin and one phthalocyanine derivatives on thin ZnO film was studied by monitoring absorption spectra of the samples. The compounds were equipped with carboxylic or phosphate groups to bind to the surface. The SAM formation was found to be fast. The layer was formed in less than 15 min for all studied porphyrins, and 30 min was sufficient to form phthalocyanine layer. For porphyrins with different anchor groups the SAM formation was too fast to see any difference between the anchoring groups. The stability of SAMs was tested then by immersing the samples into neat solvents. Upon immersion the SAMs were gradually losing the absorbance for all the compounds with degradation trends being in line with p[Formula: see text] values of the binding groups of the same type. However, even for the weakest binding group the SAM was relatively stable after a few tens of minutes of washing, which was sufficient to remove physisorbed compounds but the SAM was essentially not destroyed. Comparison of SAMs on thin films with SAMs on ZnO nanorods and TiO2 nanoparticle films indicated the same fast layer formation but relatively weaker SAMs stability, showing 20–40% faster absorption losses during the washing.

1-Propanethiol is chosen as a model alkanethiol to probe detailed mechanisms of the self-assembled monolayer (SAM) formation at aqueous/Au(111) interfaces. The assembly processes, including initial physi- and chemisorption, pit formation, and domain growth, were recorded into movies in real-time with high resolution by in situ scanning tunneling microscopy (STM) under potential control. Two major adsorption steps were disclosed in the propanethiol SAM formation. The first step involves weak interactions accompanied by the lift of the Au(111) surface reconstruction, which depends reversibly on the electrochemical potentials. The second step is chemisorption to form a dense monolayer, accompanied by formation of pits as well as structural changes in the terrace edges. Pits emerged at the stage of the reconstruction lift and increased to a maximum surface coverage of 4.0 +/- 0.4% at the completion of the SAM formation. Well-defined triangular pits in the SAM were found on the large terraces (more than 300 nm wide), whereas few and small pinholes appeared at the terrace edge areas. Smooth edges were converted into saw-like structural features during the SAM formation, primarily along the Au(111) atomic rows. These observations suggest that shrinking and rearrangement of gold atoms are responsible for both formation of the pits and the shape changes of the terrace edges. STM images disclose a (2 square root 3 x 3)R30 degrees periodic lattice within the ordered domains. Along with electrochemical measurements, each lattice unit is assigned to contain four propanethiol molecules exhibiting different electronic contrasts, which might originate in different surface orientations of the adsorbed molecules.

The formation of self-assembled monolayers (SAMs) of representative thiocarbohydrate derivatives onto a gold surface has been investigated to build an artificial carbohydrate scaffold to mimic non-bonded molecular recognition phenomena. Three types of carbohydrate SAMs were formulated from (i) 1-β-d-thioglucose (1), (ii) 1-β-d-thioglucose tetraacetate (2), and (iii) 2-mercaptoethyl α-d-mannopyranoside (3). Subsequently, each SAM was spectroscopically characterized by reflection-absorption infrared spectroscopy (RAIRS). Deprotection of the acylated carbohydrate SAM was achieved in situ, indicating that chemical transformation may be performed without disruption of the sulfurgold bond. With the mannose derivative, in which the carbohydrate moiety was separated from the gold surface by the spacer unit OCH2CH2SH, it was possible to demonstrate that such a carbohydrate SAM was able to interact selectively with a specific carbohydrate binding protein, i.e., concanavalin A (Con A). Exposure of the mannose derive...

A series of three Phthalocyanine (Pc) derivatives have been designed, synthesised and formulated as self-assembled monolayers (SAMs) on gold-coated optical waveguides. The alkyl chain tethering the Pc macrocycles to the gold surface via a thiol moiety varied in length viz. (CH2)11, (CH2)8 and (CH2)3. The three Pc SAMs have been characterised using reflection absorption infrared spectroscopy and fluorescence spectroscopy excited via the evanescent wave. The infrared data have shown that the length of the alkyl tether has a profound effect on the orientation and packing density of the Pc macrocycle on the gold surface. Similarly, the intensity of fluorescence observed from the Pc monolayers was related to the length of the alkyl tether. A further investigation of the C11 Pc derivative SAM has shown that the monolayer film was stable, exhibiting no oxidation and only minor orientation changes on the gold surface over a period of 24 months as determined by infrared and fluorescence spectroscopy. The longevity of the Pc SAM is thought to be due to the macrocyclic ring possibly preventing oxidation of the thiolate root. As simple alkanethiols are known to oxidise at gold surfaces, the stability results obtained for the Pc derivative would suggest that macrocyclic SAMs may have properties that are more suitable for long term applications.

A low-current scanning tunneling microscope (STM) was used to image ordered alkanethiol self-assembled monolayers (SAMs) on Au (111) surface. The effects of the tunneling current on the STM images of both decanethiol and dodecanethiol SAMs were studied. At low current, with the tip above the sample surface, domain boundaries and ordered alkanethiol molecules can be seen clearly. When the tunneling current was increased, destructive STM images of decanethiol and dodecanethiol SAMs were observed. However, when the tunneling current was reduced back to the original low values, the ordered structures of alkanethiol molecules reappeared. This reversible process suggests that there is no rearrangement in the sulfur head groups under different tunneling current conditions. In this article, we present a model which supports the important role of the alkyl chain in the STM imaging of SAMs. In our model, the medium conductance is a key factor.

Kinetic studies of attachment and re-orientation of octyltriethoxysilane for formation of self-assembled monolayer on a silica substrate

Self-assembled monolayers (SAM) formed on gold or hydroxylated surfaces are well ordered organic surfaces that enable the control of interface property at the molecular scale. Microcontact printing is a simple technique that can pattern the formation of SAM in the plane with dimensions on the micron scale. The combination of SAM and microcontact printing makes a technique useful for studying a variety of fundamental phenomena in bio-interfacial science such as cell adhesion. However, the existence of surface roughness tends to impede the effectiveness of the method in generating the desirable interface properties. Studies have shown that surface roughness significantly changes adhesion of SAM coated material. The current study tries to understand the roughness effects on bio-adhesion of cell-SAM substratum. A current model of cell adhesion considers the effects of nonspecific and specific interactions between adhesion molecules and the substrate assuming an isotropic Gaussian distributed roughness. Simulation results show the change of pull-off force and contact area due to different scales of roughness. The reduction rate of cell adhesion due to roughness and chemical-mechanical factors are then compared to show the significance of roughness effects on SAM adhesion. Results suggest that caution must be taken in quantitative interpretation of protein and cell adsorption strength by using SAM device as a biosensor.

Metal-reducing subsurface bacteria like Geobacter sulfurreducens can reductively precipitate water-soluble uranium salts. However, very little information is available about this bacteria's uranium reduction mechanism. Most of the metabolic investigations are based on genetic analysis, where specific proteins are either deleted or overexpressed to elucidate its role in the electron transfer process. However these approaches to identify the electron carriers are limited because mutation of one gene can cause multiple phenotypic changes resulting in alterations of the native uranium reductase machinery. Yet, these limitations can be bypassed through the use of nanoscale in vitro platforms that mimic the Geobacter cell envelope electron carrier machinery. Therefore, we constructed nanostructured biomimetic interfaces equipped with Geobacter’s most abundant and conserved electron carrying cytochromes (periplasmic cytochrome PpcA and outer membrane cytochrome OmcB) to mimic the cell membrane electron transfer mechanism and adapted it to the platform capable of spectroelectrochemical determination. Spectroelectrochemical techniques combines electrochemistry and spectroscopic measurements, and offers advantage offering capability to assess changes in specific molecules in the system as a function of electric potential. We built working electrode form a transparent slide coated with gold (~100 Ao thickness) and covered with self assembled monolayer (SAM) of thiolipids. Formation of SAM on the gold electrodes shielded the protein solution from degradation at the electrode surface, and furthermore provided us with the capability of controlling the access of species in solution towards working electrode. Redox activity of Geobacter cytochrome c PpcA was measured electrochemically by technique like cyclic voltammetry and chronoamperometry, where changes in current at the working electrode are monitored as a function of applied potential. High transparency of the working electrode allowed us to measure reduction of PpcA spectrophotometrically by presence of three characteristic absorption bands, called Soret or gamma peak which shift from ~408 in oxidized form to ~420 in reduced form, alpha (α) peak at ~ 552 nm and beta (β) at ~ 521 nm. The cytochrome was immobilized onto a mixed self assembled monolayer of alkanethiols on a gold electrode. The ratio of carboxy acid terminating alkane group to alcohol terminating alkane group was optimized for the immobilization of protein in active conformation. Immobilized PpcA was characterized electrochemically by cyclic voltammetry, chronoamperometry and square wave voltammetry. Immobilized PpcA showed stable electrochemical response and was capable of being redox active in the immobilized state. The midpoint redox potential of immobilized PpcA was -372 mV vs. Ag/AgCl, also within the orders obtained for PpcA in solution (-374 mV vs. Ag/AgCl). Thus the immobilized PpcA at the SAM electrode was capable of direct electron transfer without any need of mediator resulting precise control over electrochemical potential. Based on the hypothesis that PpcA may be transfer electrons produced in respiration to OmcB as part of Geobacter’s electron transport chain, we attempted to demonstrate electron transfer from PpcA to OmcB in optically transparent thin layer cell. Addition of OmcB-containing membrane vesicles to the PpcA, yielded a small increase in the CV peak of PpcA. Since OmcB membrane vesicles, are not capable of direct electron transfer to and from the electrode, the increase in the current can be attributed to the catalytic reduction of OmcB by reduced PpcA. Redox spectra of the cytochromes monitored in the multipotential step experiments showed additional evidence of reduction of OmcB from PpcA. Change were observed in the Soret Peak at 410 and 420 nm, and 552 peaks as a function of electrode potential. The biomimetic system assembled here was intended to simulate electron transfer within Geobacter’s cell envelope, in which electrons produced in respiration are transferred from the inner membrane (mimicked by the SAM coated gold electrode) through the periplasm (mimicked by the PpcA layer bound to the SAM) to outer membrane cytochromes (mimicked by the OmcB-containing microsomes. This study’s establishment of a biomimetic redox-active cell envelope (BRACE) provides a new research platform with which to study Geobacter electron transport to extracellular electron acceptors. This nanoplatform integrating the key components of Geobacter’s electron transfer machinery will allow us to study the activity of native redox components in a controllable system. The information obtained about the redox interaction between cytochrome provides interesting insights about the mechanism of electron transfer in Geobacter which may lead to more successful strategies for groundwater uranium fixation.

Barrier height of self-assembled monolayers (SAMs) on Au(111) was measured using scanning tunneling microscopy (STM) with a vertical modulation. We obtained nanometer scale STM images of alkanethiol SAMs, and binary component SAM films fabricated by an implantation technique. Local barrier height on the alkanethiol SAM at the depressions and the domain boundaries is larger than that on the domains where the molecular lattice is visible, probably due to the molecular density or orientation. A molecular resolution contrast was obtained at a conjugated molecule embedded in the alkanethiol SAM, reflecting the difference in the molecular species. We found that the tip-sample interaction force affects the barrier height measurements, especially when the tunneling gap is small, e.g., on nonanethiol SAM at the tunneling resistance smaller than 50 GΩ.

This paper describes the preparation of oligo(ethylene glycol)-terminated alkanethiols having structure HS- (CHz)'l(OCH2CHz),nOH (m = 3-7) and their use in the formation of self-assembled monolayers (SAMs) on gold. A combination of experimental evidence derived from X-ray photoelectron sp€ctroscopy (XPS), measurement of contact angles, and ellipsometry implies substantial disorder in the oligo(ethylene glycol)-containing segment. The order in the -(CHz)r- group is not defined by the available evidence. The SAMs are moderately hydrophilic: du(H2O) = 34-38o; d,(H2O) = 22-25. A study of monolayers containing mixtures of HS(CH2)rrCHr and HS(CH2)rr(OCH2CH 2)6OH suggests that the oligo(ethylene glycol) moieties are eflective at preventing underlying methylene groups from influencing wetting by water. A limited study demonstrates that these oligo(ethylene glycol)-containing SAMs resist the adsorption of protein from solution and suggests that SAMs will be a useful model system for studying the adsorption of proteins onto organic surfaces.